MTA2
metastasis associated 1 family member 2, the group of GATA zinc finger domain containing|NuRD complex subunits|Myb/SANT domain containing
Basic information
Region (hg38): 11:62593214-62601865
Previous symbols: [ "MTA1L1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTA2 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 19 | 19 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 20 | 0 | 0 |
Variants in MTA2
This is a list of pathogenic ClinVar variants found in the MTA2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 11-62593943-G-C | not specified | Uncertain significance (Jul 14, 2021) | ||
| 11-62593951-G-A | not specified | Uncertain significance (Oct 18, 2021) | ||
| 11-62593958-G-T | not specified | Uncertain significance (Dec 20, 2023) | ||
| 11-62593994-G-A | not specified | Uncertain significance (Feb 15, 2023) | ||
| 11-62594007-C-T | not specified | Uncertain significance (Nov 05, 2021) | ||
| 11-62594344-T-C | not specified | Uncertain significance (Oct 26, 2022) | ||
| 11-62594349-C-T | not specified | Uncertain significance (Jul 09, 2021) | ||
| 11-62594556-C-T | not specified | Uncertain significance (Dec 27, 2023) | ||
| 11-62594557-G-A | not specified | Uncertain significance (Dec 21, 2022) | ||
| 11-62594601-C-T | not specified | Uncertain significance (Aug 04, 2021) | ||
| 11-62594993-C-T | not specified | Uncertain significance (Oct 22, 2021) | ||
| 11-62595047-C-T | not specified | Uncertain significance (Nov 18, 2022) | ||
| 11-62595452-T-G | not specified | Uncertain significance (Dec 17, 2023) | ||
| 11-62595763-G-A | not specified | Uncertain significance (Sep 17, 2021) | ||
| 11-62595840-C-T | not specified | Uncertain significance (Mar 23, 2022) | ||
| 11-62596325-C-A | not specified | Uncertain significance (Nov 10, 2022) | ||
| 11-62596489-A-G | not specified | Uncertain significance (May 11, 2022) | ||
| 11-62596735-G-A | not specified | Uncertain significance (Dec 20, 2023) | ||
| 11-62597678-C-G | not specified | Uncertain significance (Jan 24, 2024) | ||
| 11-62598556-G-C | not specified | Uncertain significance (Jan 26, 2022) | ||
| 11-62600178-C-T | not specified | Uncertain significance (May 07, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MTA2 | protein_coding | protein_coding | ENST00000278823 | 18 | 8627 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.745 | 0.255 | 125586 | 0 | 162 | 125748 | 0.000644 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.13 | 224 | 400 | 0.560 | 0.0000235 | 4309 |
| Missense in Polyphen | 53 | 144 | 0.36806 | 1683 | ||
| Synonymous | -0.852 | 157 | 144 | 1.09 | 0.00000753 | 1358 |
| Loss of Function | 4.66 | 8 | 39.7 | 0.202 | 0.00000209 | 444 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00163 | 0.00152 |
| Ashkenazi Jewish | 0.000312 | 0.000298 |
| East Asian | 0.00147 | 0.00141 |
| Finnish | 0.000613 | 0.000601 |
| European (Non-Finnish) | 0.000768 | 0.000730 |
| Middle Eastern | 0.00147 | 0.00141 |
| South Asian | 0.0000996 | 0.0000980 |
| Other | 0.000344 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in the regulation of gene expression as repressor and activator. The repression might be related to covalent modification of histone proteins.;
- Pathway
- ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression;Positive epigenetic regulation of rRNA expression;Signal Transduction;Epigenetic regulation of gene expression;Gene expression (Transcription);Generic Transcription Pathway;HDACs deacetylate histones;RNA Polymerase I Promoter Clearance;RNA Polymerase II Transcription;Chromatin modifying enzymes;RNA Polymerase I Transcription;RNA Polymerase I Transcription Initiation;EGFR1;Regulation of PTEN gene transcription;PTEN Regulation;PIP3 activates AKT signaling;Chromatin organization;Regulation of TP53 Activity through Acetylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Intracellular signaling by second messengers;Signaling events mediated by HDAC Class I
(Consensus)
Recessive Scores
- pRec
- 0.278
Intolerance Scores
- loftool
- 0.204
- rvis_EVS
- -1.02
- rvis_percentile_EVS
- 7.94
Haploinsufficiency Scores
- pHI
- 0.896
- hipred
- Y
- hipred_score
- 0.809
- ghis
- 0.627
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.768
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mta2
- Phenotype
- immune system phenotype; renal/urinary system phenotype; skeleton phenotype; liver/biliary system phenotype; hematopoietic system phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); craniofacial phenotype; homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;DNA methylation;chromatin assembly or disassembly;regulation of fibroblast migration;histone deacetylation;ATP-dependent chromatin remodeling;positive regulation of transcription by RNA polymerase II
- Cellular component
- histone deacetylase complex;nuclear chromatin;nucleus;nucleoplasm;transcription factor complex;membrane;NuRD complex;protein-containing complex
- Molecular function
- transcription regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase II transcription factor binding;RNA polymerase II repressing transcription factor binding;transcription coactivator activity;transcription corepressor activity;histone deacetylase activity;protein binding;zinc ion binding;nucleosomal DNA binding;histone deacetylase binding